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Search Results: 1 - 10 of 415005 matches for " Eric J. B. von Wettberg "
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Early Developmental Responses to Seedling Environment Modulate Later Plasticity to Light Spectral Quality
Eric J. B. von Wettberg, John R. Stinchcombe, Johanna Schmitt
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034121
Abstract: Correlations between developmentally plastic traits may constrain the joint evolution of traits. In plants, both seedling de-etiolation and shade avoidance elongation responses to crowding and foliage shade are mediated by partially overlapping developmental pathways, suggesting the possibility of pleiotropic constraints. To test for such constraints, we exposed inbred lines of Impatiens capensis to factorial combinations of leaf litter (which affects de-etiolation) and simulated foliage shade (which affects phytochrome-mediated shade avoidance). Increased elongation of hypocotyls caused by leaf litter phenotypically enhanced subsequent elongation of the first internode in response to low red:far red (R:FR). Trait expression was correlated across litter and shade conditions, suggesting that phenotypic effects of early plasticity on later plasticity may affect variation in elongation traits available to selection in different light environments.
Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives
Mulualem T. Kassa, R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Birinchi K. Sarma, Subhojit Datta, Hari D. Upadhyaya, Rajeev K. Varshney, Eric J. B. von Wettberg, Douglas R. Cook
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039563
Abstract: Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during pigeonpea domestication.
Genomic Analysis of Differentiation between Soil Types Reveals Candidate Genes for Local Adaptation in Arabidopsis lyrata
Thomas L. Turner, Eric J. von Wettberg, Sergey V. Nuzhdin
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003183
Abstract: Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low Ca:Mg ratio in A. lyrata.
Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers
Manish Roorkiwal, Eric J. von Wettberg, Hari D. Upadhyaya, Emily Warschefsky, Abhishek Rathore, Rajeev K. Varshney
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102016
Abstract: To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past.
Conclusions about Niche Expansion in Introduced Impatiens walleriana Populations Depend on Method of Analysis
Lisa Mandle,Dan L. Warren,Matthias H. Hoffmann,A. Townsend Peterson,Johanna Schmitt,Eric J. von Wettberg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015297
Abstract: Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas.
Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs
Rachit K. Saxena, Eric von Wettberg, Hari D. Upadhyaya, Vanessa Sanchez, Serah Songok, Kulbhushan Saxena, Paul Kimurto, Rajeev K. Varshney
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088568
Abstract: Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
The 55 Cancri Planetary System: Fully Self-Consistent N-body Constraints and a Dynamical Analysis
Benjamin E. Nelson,Eric B. Ford,Jason T. Wright,Debra A. Fischer,Kasper von Braun,Andrew W. Howard,Matthew J. Payne,Saleh Dindar
Physics , 2014, DOI: 10.1093/mnras/stu450
Abstract: We present an updated study of the planets known to orbit 55 Cancri A using 1,418 high-precision radial velocity observations from four observatories (Lick, Keck, Hobby-Eberly Telescope, Harlan J. Smith Telescope) and transit time/durations for the inner-most planet, 55 Cancri "e" (Winn et al. 2011). We provide the first posterior sample for the masses and orbital parameters based on self-consistent n-body orbital solutions for the 55 Cancri planets, all of which are dynamically stable (for at least $10^8$ years). We apply a GPU version of Radial velocity Using N-body Differential evolution Markov Chain Monte Carlo (RUN DMC; B. Nelson et al. 2014) to perform a Bayesian analysis of the radial velocity and transit observations. Each of the planets in this remarkable system has unique characteristics. Our investigation of high-cadence radial velocities and priors based on space-based photometry yields an updated mass estimate for planet "e" ($8.09\pm0.26$ M$_\oplus$), which affects its density ($5.51\pm^{1.32}_{1.00}$ g cm$^{-3}$) and inferred bulk composition. Dynamical stability dictates that the orbital plane of planet "e" must be aligned to within $60^o$ of the orbital plane of the outer planets (which we assume to be coplanar). The mutual interactions between the planets "b" and "c" may develop an apsidal lock about $180^o$. We find 36-45% of all our model systems librate about the anti-aligned configuration with an amplitude of $51^o\pm^{6^o}_{10^o}$. Other cases showed short-term perturbations in the libration of $\varpi_b-\varpi_c$, circulation, and nodding, but we find the planets are not in a 3:1 mean-motion resonance. A revised orbital period and eccentricity for planet "d" pushes it further toward the closest known Jupiter analog in the exoplanet population.
Reducing Medical Costs and Improving Quality via Self-Management Tools
Harold J DeMonaco ,Eric von Hippel
PLOS Medicine , 2007, DOI: 10.1371/journal.pmed.0040104
Abstract:
Interspecific Differences between D. pulex and D. magna in Tolerance to Cyanobacteria with Protease Inhibitors
Christian J. Kuster, Eric Von Elert
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062658
Abstract: It is known that cyanobacteria negatively affect herbivores due to their production of toxins such as protease inhibitors. In the present study we investigated potential interspecific differences between two major herbivores, Daphnia magna and Daphnia pulex, in terms of their tolerance to cyanobacteria with protease inhibitors. Seven clones each of D. magna and of D. pulex were isolated from different habitats in Europe and North America. To test for interspecific differences in the daphnids’ tolerance to cyanobacteria, their somatic and population growth rates were determined for each D. magna and D. pulex clone after exposure to varying concentrations of two Microcystis aeruginosa strains. The M. aeruginosa strains NIVA and PCC? contained either chymotrypsin or trypsin inhibitors, but no microcystins. Mean somatic and population growth rates on a diet with 20% NIVA were significantly more reduced in D. pulex than in D. magna. On a diet with 10% PCC?, the population growth of D. pulex was significantly more reduced than that of D. magna. This indicates that D. magna is more tolerant to cyanobacteria with protease inhibitors than D. pulex. The reduction of growth rates was possibly caused by an interference of cyanobacterial inhibitors with proteases in the gut of Daphnia, as many other conceivable factors, which might have been able to explain the reduced growth, could be excluded as causal factors. Protease assays revealed that the sensitivities of chymotrypsins and trypsins to cyanobacterial protease inhibitors did not differ between D. magna and D. pulex. However, D. magna exhibited a 2.3-fold higher specific chymotrypsin activity than D. pulex, which explains the observed higher tolerance to cyanobacterial protease inhibitors of D. magna. The present study suggests that D. magna may control the development of cyanobacterial blooms more efficiently than D. pulex due to differences in their tolerance to cyanobacteria with protease inhibitors.
The Discovery of HD 37605c and a Dispositive Null Detection of Transits of HD 37605b
Sharon Xuesong Wang,Jason T. Wright,William Cochran,Stephen R. Kane,Gregory W. Henry,Matthew J. Payne,Michael Endl,Phillip J. MacQueen,Jeff A. Valenti,Victoria Antoci,Diana Dragomir,Jaymie M. Matthews,Andrew W. Howard,Geoffrey W. Marcy,Howard Isaacson,Eric B. Ford,Suvrath Mahadevan,Kaspar von Braun
Physics , 2012, DOI: 10.1088/0004-637X/761/1/46
Abstract: We report the radial-velocity discovery of a second planetary mass companion to the K0 V star HD 37605, which was already known to host an eccentric, P~55 days Jovian planet, HD 37605b. This second planet, HD 37605c, has a period of ~7.5 years with a low eccentricity and an Msini of ~3.4 MJup. Our discovery was made with the nearly 8 years of radial velocity follow-up at the Hobby-Eberly Telescope and Keck Observatory, including observations made as part of the Transit Ephemeris Refinement and Monitoring Survey (TERMS) effort to provide precise ephemerides to long-period planets for transit follow-up. With a total of 137 radial velocity observations covering almost eight years, we provide a good orbital solution of the HD 37605 system, and a precise transit ephemeris for HD 37605b. Our dynamic analysis reveals very minimal planet-planet interaction and an insignificant transit time variation. Using the predicted ephemeris, we performed a transit search for HD 37605b with the photometric data taken by the T12 0.8-m Automatic Photoelectric Telescope (APT) and the Microvariability and Oscillations of Stars (MOST) satellite. Though the APT photometry did not capture the transit window, it characterized the stellar activity of HD 37605, which is consistent of it being an old, inactive star, with a tentative rotation period of 57.67 days. The MOST photometry enabled us to report a dispositive null detection of a non-grazing transit for this planet. Within the predicted transit window, we exclude an edge-on predicted depth of 1.9% at >>10sigma, and exclude any transit with an impact parameter b>0.951 at greater than 5sigma. We present the BOOTTRAN package for calculating Keplerian orbital parameter uncertainties via bootstrapping. We found consistency between our orbital parameters calculated by the RVLIN package and error bars by BOOTTRAN with those produced by a Bayesian analysis using MCMC.
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